+Open data
-Basic information
Entry | Database: PDB / ID: 8i9m | ||||||
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Title | The RAGE and HMGB1 complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / RAGE / HMGB1 / Inflammation | ||||||
Function / homology | Function and homology information regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / negative regulation of apoptotic cell clearance / advanced glycation end-product receptor activity / positive regulation of endothelin production / negative regulation of RNA polymerase II transcription preinitiation complex assembly ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / negative regulation of apoptotic cell clearance / advanced glycation end-product receptor activity / positive regulation of endothelin production / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / regulation of T cell mediated cytotoxicity / myeloid dendritic cell activation / glucose mediated signaling pathway / T-helper 1 cell activation / negative regulation of long-term synaptic depression / C-X-C chemokine binding / T-helper 1 cell differentiation / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of dendritic cell differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / regulation of p38MAPK cascade / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / regulation of non-canonical NF-kappaB signal transduction / positive regulation of DNA ligation / positive regulation of interleukin-1 production / RAGE receptor binding / Regulation of TLR by endogenous ligand / scavenger receptor activity / alphav-beta3 integrin-HMGB1 complex / induction of positive chemotaxis / bubble DNA binding / V(D)J recombination / transcytosis / protein localization to membrane / Apoptosis induced DNA fragmentation / positive regulation of monocyte chemotactic protein-1 production / inflammatory response to antigenic stimulus / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / supercoiled DNA binding / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / apoptotic cell clearance / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / dendritic cell chemotaxis / laminin receptor activity / positive regulation of p38MAPK cascade / DNA binding, bending / positive regulation of vascular endothelial cell proliferation / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / phosphatidylserine binding / chemoattractant activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / response to amyloid-beta / DNA topological change / TRAF6 mediated NF-kB activation / positive regulation of interleukin-10 production / Advanced glycosylation endproduct receptor signaling / negative regulation of blood vessel endothelial cell migration / negative regulation of type II interferon production / transport across blood-brain barrier / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of long-term synaptic potentiation / positive regulation of blood vessel endothelial cell migration / positive regulation of DNA binding / Pyroptosis / positive regulation of autophagy / heterochromatin formation / DNA polymerase binding / four-way junction DNA binding / positive regulation of chemokine production / condensed chromosome / positive regulation of interleukin-12 production / activation of innate immune response / transcription repressor complex / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / lipopolysaccharide binding / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / regulation of synaptic plasticity / fibrillar center / autophagy / response to wounding / double-strand break repair via nonhomologous end joining / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / transmembrane signaling receptor activity / transcription corepressor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.19 Å | ||||||
Authors | Han, C.W. / Kim, H.J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The RAGE and HMGB1 complex Authors: Han, C.W. / Kim, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i9m.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i9m.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 8i9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i9m_validation.pdf.gz | 966.6 KB | Display | wwPDB validaton report |
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Full document | 8i9m_full_validation.pdf.gz | 985 KB | Display | |
Data in XML | 8i9m_validation.xml.gz | 26 KB | Display | |
Data in CIF | 8i9m_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/8i9m ftp://data.pdbj.org/pub/pdb/validation_reports/i9/8i9m | HTTPS FTP |
-Related structure data
Related structure data | 35276MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 8590.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HMGB1, HMG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09429 |
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#2: Protein | Mass: 23068.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli (E. coli) / References: UniProt: Q15109 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The RAGE and HMGB1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.50 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 39.99 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121467 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: CDL v1.2 | ||||||||||||||||||||||||
Refine LS restraints |
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